TinkerCell：用于合成生物学的模块化CAD工具
TinkerCell: Modular CAD Tool for Synthetic Biology
摘要：
合成生物学汇集了工程学和生物学的概念和技术。在这一领域，计算机辅助设计（CAD）是必要的，以弥合计算建模和生物学数据之间的差距。已经创建了一个名为TinkerCell的应用程序，以作为合成生物学的CAD工具。TinkerCell是一个可视化建模工具，支持生物部分的层次结构。此层次结构中的每个部件都由一组定义部件的属性（如序列或速率常数）组成。使用这些部分构建的模型可以使用TinkerCell通过广泛的C和Python API托管的各种C和Python程序进行分析。TinkerCell支持模块的概念，模块是具有接口的网络。这些模块可以相互连接，形成更大的模块化网络。由于TinkerCell将模型中的参数和方程与其各自的零件相关联，因此可以从数据库中加载零件及其参数和速率方程。模块化网络设计可用于交换模块以及测试生物系统中的模块化概念。灵活的建模框架以及C和Python API允许TinkerCell作为众多第三方算法的宿主。TinkerCell是一个基于Berkeley Software Distribution许可证的免费开源项目。下载、文档和教程可在www.tinkercell.com上获得。
英文摘要：
Synthetic biology brings together concepts and techniques from engineering and biology. In this field, computer-aided design (CAD) is necessary in order to bridge the gap between computational modeling and biological data. An application named TinkerCell has been created in order to serve as a CAD tool for synthetic biology. TinkerCell is a visual modeling tool that supports a hierarchy of biological parts. Each part in this hierarchy consists of a set of attributes that define the part, such as sequence or rate constants. Models that are constructed using these parts can be analyzed using various C and Python programs that are hosted by TinkerCell via an extensive C and Python API. TinkerCell supports the notion of a module, which are networks with interfaces. Such modules can be connected to each other, forming larger modular networks. Because TinkerCell associates parameters and equations in a model with their respective part, parts can be loaded from databases along with their parameters and rate equations. The modular network design can be used to exchange modules as well as test the concept of modularity in biological systems. The flexible modeling framework along with the C and Python API allows TinkerCell to serve as a host to numerous third-party algorithms. TinkerCell is a free and open-source project under the Berkeley Software Distribution license. Downloads, documentation, and tutorials are available at www.tinkercell.com.
机构、总结、中文摘要均由AI分析而来，可能存在错误，请以论文正文为准。
